Chapter 4 Community composition
4.1 Taxonomy overview
4.1.1 Stacked barplot
genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
filter(count > 0) %>% #filter 0 counts
ggplot(., aes(x=sample,y=count, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors) +
facet_nested(. ~ Location + Origin, scales="free") + #facet per day and treatment
guides(fill = guide_legend(ncol = 1)) +
theme(axis.text.x = element_blank(),
axis.ticks.x =element_blank(),
axis.title.x = element_blank(),
axis.text.y = element_text(size=8),
axis.title.y = element_text(size=12),
panel.background = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
panel.border = element_rect(colour = "black", fill = NA),
strip.background = element_rect(fill = "white", color = "black"),
strip.text = element_text(size = 12, lineheight = 0.6)) +
labs(fill="Phylum",y = "Relative abundance",x="Samples")4.1.2 Phylum relative abundances
phylum_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
left_join(genome_metadata, by = join_by(genome == genome)) %>%
group_by(sample,phylum) %>%
summarise(relabun=sum(count))
phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| phylum | mean | sd |
|---|---|---|
| Bacteroidota | 0.3174419111 | 0.183019959 |
| Bacillota_A | 0.1950249672 | 0.120311961 |
| Actinomycetota | 0.1816628641 | 0.164661070 |
| Pseudomonadota | 0.0906110310 | 0.129035667 |
| Campylobacterota | 0.0753140001 | 0.122740598 |
| Bacillota_C | 0.0657125307 | 0.090589426 |
| Bacillota | 0.0558322249 | 0.084087344 |
| Fusobacteriota | 0.0169238273 | 0.036464401 |
| Desulfobacterota | 0.0012635896 | 0.004283801 |
| Cyanobacteria | 0.0002130539 | 0.001747414 |
phylum_arrange <- phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun)) %>%
arrange(-mean) %>%
select(phylum) %>%
pull()
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[rev(phylum_arrange)]) +
geom_jitter(alpha=0.5) +
theme_minimal() +
theme(legend.position="none") +
labs(y="Phylum",x="Relative abundance")4.1.3 Phylum percentages by behaviour
Tame cats
| Phylum | mean | sd |
|---|---|---|
| Bacteroidota | 32.56152690 | 17.0735823 |
| Bacillota_A | 19.43901972 | 9.2325815 |
| Actinomycetota | 18.15297600 | 14.6097544 |
| Pseudomonadota | 8.58500960 | 8.8366787 |
| Campylobacterota | 7.99160260 | 11.4635975 |
| Bacillota_C | 7.03812491 | 9.0283540 |
| Bacillota | 4.78213672 | 6.8948853 |
| Fusobacteriota | 1.24402612 | 1.8499876 |
| Desulfobacterota | 0.17332897 | 0.3125926 |
| Cyanobacteria | 0.03224846 | 0.2207708 |
Feral cats
| Phylum | mean | sd |
|---|---|---|
| Bacteroidota | 28.216582864 | 17.60825972 |
| Bacillota_A | 24.008928630 | 11.57531069 |
| Actinomycetota | 17.469038917 | 14.43475736 |
| Pseudomonadota | 8.640301288 | 12.50709604 |
| Bacillota_C | 7.456856533 | 8.95839921 |
| Bacillota | 7.173243065 | 8.66411699 |
| Campylobacterota | 4.450683081 | 6.19179683 |
| Fusobacteriota | 2.234878008 | 4.15301854 |
| Desulfobacterota | 0.342681443 | 0.81138291 |
| Cyanobacteria | 0.006806171 | 0.03760557 |
4.2 Taxonomy boxplot
4.2.1 Family
family_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,family) %>%
summarise(relabun=sum(count))
family_summary %>%
group_by(family) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| family | mean | sd |
|---|---|---|
| Bacteroidaceae | 2.957679e-01 | 0.1794702282 |
| Lachnospiraceae | 1.072346e-01 | 0.0913528566 |
| Coriobacteriaceae | 9.631433e-02 | 0.1009342181 |
| Helicobacteraceae | 5.410633e-02 | 0.1022560566 |
| Megasphaeraceae | 3.895540e-02 | 0.0732948425 |
| Enterobacteriaceae | 3.671005e-02 | 0.1156492986 |
| Bifidobacteriaceae | 3.634821e-02 | 0.0642309973 |
| Succinivibrionaceae | 3.534985e-02 | 0.0599537024 |
| Ruminococcaceae | 3.408006e-02 | 0.0348433297 |
| Actinomycetaceae | 3.080463e-02 | 0.0930244958 |
| Campylobacteraceae | 2.120767e-02 | 0.0374825084 |
| Lactobacillaceae | 2.056464e-02 | 0.0600942736 |
| Fusobacteriaceae | 1.692383e-02 | 0.0364644007 |
| Clostridiaceae | 1.655096e-02 | 0.0573573568 |
| Burkholderiaceae | 1.538244e-02 | 0.0157737872 |
| Atopobiaceae | 1.510044e-02 | 0.0393574894 |
| Erysipelotrichaceae | 1.498819e-02 | 0.0297202782 |
| Porphyromonadaceae | 1.231678e-02 | 0.0490743570 |
| Oscillospiraceae | 1.169099e-02 | 0.0154660823 |
| Dialisteraceae | 1.109249e-02 | 0.0168027270 |
| Peptoniphilaceae | 1.027007e-02 | 0.0377623762 |
| Streptococcaceae | 1.009343e-02 | 0.0465284432 |
| Selenomonadaceae | 9.051718e-03 | 0.0152538557 |
| Acidaminococcaceae | 6.612925e-03 | 0.0134491243 |
| Erysipelatoclostridiaceae | 6.598637e-03 | 0.0107938056 |
| Peptostreptococcaceae | 6.477379e-03 | 0.0101260977 |
| Anaerovoracaceae | 4.239616e-03 | 0.0103079362 |
| Tannerellaceae | 3.414585e-03 | 0.0079108669 |
| Pasteurellaceae | 2.963621e-03 | 0.0184648739 |
| Enterococcaceae | 2.804985e-03 | 0.0085239000 |
| Mycobacteriaceae | 2.785187e-03 | 0.0190576068 |
| Rikenellaceae | 2.616836e-03 | 0.0106713550 |
| Acutalibacteraceae | 2.198544e-03 | 0.0044303862 |
| Marinifilaceae | 2.086026e-03 | 0.0055223355 |
| Butyricicoccaceae | 1.463315e-03 | 0.0031506247 |
| Desulfovibrionaceae | 1.263590e-03 | 0.0042838013 |
| Muribaculaceae | 9.291851e-04 | 0.0040885460 |
| UBA660 | 6.460679e-04 | 0.0035734633 |
| Anaerotignaceae | 5.353989e-04 | 0.0025028446 |
| Barnesiellaceae | 3.105707e-04 | 0.0011701232 |
| UMGS124 | 3.100703e-04 | 0.0017862741 |
| Gastranaerophilaceae | 2.130539e-04 | 0.0017474140 |
| CAG-508 | 2.052995e-04 | 0.0007194205 |
| CAG-239 | 2.050753e-04 | 0.0018010322 |
| CAG-826 | 1.362811e-04 | 0.0007776869 |
| UBA1381 | 7.878665e-05 | 0.0007556950 |
family_arrange <- family_summary %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(family) %>%
pull()
# Per origin
family_summary %>%
left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5) +
facet_grid(.~Origin)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")# Per location
family_summary %>%
left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5) +
facet_grid(.~Location)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")4.2.2 Genus
genus_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,phylum,genus) %>%
summarise(relabun=sum(count)) %>%
filter(genus != "g__") %>%
mutate(genus= sub("^g__", "", genus))
genus_summary_sort <- genus_summary %>%
group_by(genus) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean)
genus_summary_sort %>%
tt()| genus | mean | sd |
|---|---|---|
| Prevotella | 1.364856e-01 | 0.1353999322 |
| Collinsella | 9.631433e-02 | 0.1009342181 |
| Phocaeicola | 8.993433e-02 | 0.0955977240 |
| Bacteroides | 5.173169e-02 | 0.0635714050 |
| Megasphaera | 3.869704e-02 | 0.0730748863 |
| Helicobacter_B | 3.657334e-02 | 0.0843378196 |
| Bifidobacterium | 3.634821e-02 | 0.0642309973 |
| Anaerobiospirillum | 3.459305e-02 | 0.0599454952 |
| Escherichia | 3.275523e-02 | 0.1083759749 |
| Roseburia | 2.314992e-02 | 0.0533913900 |
| Campylobacter_D | 2.120767e-02 | 0.0374825084 |
| Blautia_A | 2.051642e-02 | 0.0231346773 |
| Pauljensenia | 1.977626e-02 | 0.0800352518 |
| Negativibacillus | 1.819490e-02 | 0.0215815280 |
| Prevotellamassilia | 1.738141e-02 | 0.0343949273 |
| Helicobacter_A | 1.713427e-02 | 0.0507397988 |
| Clostridium_P | 1.645501e-02 | 0.0573123071 |
| Fusobacterium_B | 1.469492e-02 | 0.0345732902 |
| Sutterella | 1.425550e-02 | 0.0152994499 |
| Blautia | 1.333921e-02 | 0.0183592066 |
| UBA7748 | 1.330938e-02 | 0.0382333948 |
| Porphyromonas_A | 1.231678e-02 | 0.0490743570 |
| Trueperella | 1.102837e-02 | 0.0501260208 |
| Ligilactobacillus | 1.038602e-02 | 0.0327671906 |
| Dialister | 1.031903e-02 | 0.0157533129 |
| Streptococcus | 9.357277e-03 | 0.0446998121 |
| Gemmiger | 8.872488e-03 | 0.0146460260 |
| Holdemanella | 8.793459e-03 | 0.0187067258 |
| Lactobacillus | 8.261034e-03 | 0.0348551627 |
| Clostridium_Q | 7.967312e-03 | 0.0129501748 |
| Ruminococcus_B | 7.491864e-03 | 0.0133624741 |
| Megamonas | 6.998825e-03 | 0.0128982165 |
| Peptacetobacter | 6.477379e-03 | 0.0101260977 |
| Catenibacterium | 6.451673e-03 | 0.0106973049 |
| Faecalimonas | 6.214440e-03 | 0.0112084591 |
| Faecalibacterium | 6.206186e-03 | 0.0133252461 |
| Bulleidia | 6.127964e-03 | 0.0165765313 |
| Lawsonibacter | 5.743270e-03 | 0.0087015993 |
| Peptoniphilus_A | 4.928663e-03 | 0.0217722683 |
| Acidaminococcus | 4.738436e-03 | 0.0131157898 |
| Eisenbergiella | 4.302829e-03 | 0.0073261825 |
| Plesiomonas | 3.954812e-03 | 0.0176151160 |
| Parabacteroides | 3.414585e-03 | 0.0079108669 |
| Catenibacillus | 3.242799e-03 | 0.0054534742 |
| Histophilus | 2.963621e-03 | 0.0184648739 |
| Alistipes | 2.616836e-03 | 0.0106713550 |
| CAG-81 | 2.576496e-03 | 0.0041736848 |
| Mediterraneibacter | 2.497312e-03 | 0.0073570318 |
| Sellimonas | 2.293821e-03 | 0.0042562326 |
| Dysosmobacter | 2.255402e-03 | 0.0038273521 |
| Fusobacterium_A | 2.228906e-03 | 0.0084702675 |
| Mitsuokella | 2.052893e-03 | 0.0089367483 |
| Ruminococcus_A | 2.042994e-03 | 0.0028573373 |
| Corynebacterium | 1.947467e-03 | 0.0162046636 |
| CAG-317 | 1.827371e-03 | 0.0032549462 |
| Parolsenella | 1.791055e-03 | 0.0042478478 |
| Odoribacter | 1.786646e-03 | 0.0054424090 |
| Phascolarctobacterium_A | 1.773898e-03 | 0.0045007766 |
| UMGS905 | 1.691812e-03 | 0.0039135118 |
| Limosilactobacillus | 1.637804e-03 | 0.0065016504 |
| Flavonifractor | 1.526253e-03 | 0.0030043128 |
| S5-A14a | 1.461682e-03 | 0.0086194900 |
| CAG-110 | 1.454019e-03 | 0.0077541828 |
| VUNA01 | 1.401454e-03 | 0.0054991752 |
| Butyricicoccus | 1.357370e-03 | 0.0031145926 |
| Enterococcus_B | 1.310733e-03 | 0.0059365102 |
| Schaedlerella | 1.305216e-03 | 0.0026356164 |
| Desulfovibrio | 1.146069e-03 | 0.0040502698 |
| Enterocloster | 1.081652e-03 | 0.0016014566 |
| CAG-521 | 1.044864e-03 | 0.0044915406 |
| Robinsoniella | 1.000496e-03 | 0.0022500094 |
| CAG-279 | 9.291851e-04 | 0.0040885460 |
| Enterococcus_E | 8.894621e-04 | 0.0052314621 |
| Fusicatenibacter | 8.503089e-04 | 0.0040305315 |
| Lawsonella | 8.377194e-04 | 0.0044649755 |
| Allisonella | 7.734581e-04 | 0.0017636201 |
| Lactococcus | 7.361496e-04 | 0.0045553482 |
| UMGS1370 | 7.113596e-04 | 0.0019148297 |
| Lachnospira | 6.870854e-04 | 0.0021298406 |
| Dorea_B | 6.868715e-04 | 0.0019244447 |
| Bariatricus | 6.260243e-04 | 0.0020974371 |
| UBA9502 | 6.094947e-04 | 0.0010769033 |
| Enterococcus | 6.047896e-04 | 0.0038126660 |
| UMGS1472 | 5.927633e-04 | 0.0010326554 |
| Emergencia | 5.805635e-04 | 0.0012817363 |
| Succinivibrio | 5.598203e-04 | 0.0022589496 |
| Anaerotignum | 5.353989e-04 | 0.0025028446 |
| CAG-877 | 5.310297e-04 | 0.0030198616 |
| Hungatella_A | 5.159539e-04 | 0.0024856275 |
| Evtepia | 4.179293e-04 | 0.0010548717 |
| Eubacterium_M | 3.872451e-04 | 0.0020920297 |
| Ruminococcus_C | 3.818769e-04 | 0.0021783041 |
| Anaerobutyricum | 3.713931e-04 | 0.0007790163 |
| Barnesiella | 3.105707e-04 | 0.0011701232 |
| Butyricimonas | 2.993807e-04 | 0.0011821610 |
| UMGS1872 | 2.941129e-04 | 0.0019462982 |
| Mobilibacterium | 2.870924e-04 | 0.0013257840 |
| Fournierella | 2.796504e-04 | 0.0011213974 |
| Eubacterium_H | 2.754780e-04 | 0.0018906167 |
| Caecibacter | 2.583579e-04 | 0.0011470773 |
| Clostridium_A | 2.543803e-04 | 0.0019730949 |
| Helicobacter_C | 2.498036e-04 | 0.0018283330 |
| Paraprevotella | 2.348920e-04 | 0.0018824059 |
| Latilactobacillus | 2.222007e-04 | 0.0021312745 |
| Dorea_A | 2.150652e-04 | 0.0015260870 |
| Zag111 | 2.130539e-04 | 0.0017474140 |
| CAG-354 | 2.052995e-04 | 0.0007194205 |
| CAG-495 | 2.050753e-04 | 0.0018010322 |
| Anaerobiospirillum_A | 1.969800e-04 | 0.0010117016 |
| Peptoniphilus_C | 1.797556e-04 | 0.0017241550 |
| Eubacterium_G | 1.536509e-04 | 0.0010434640 |
| Helicobacter_D | 1.489164e-04 | 0.0009489548 |
| Erysipelatoclostridium | 1.469635e-04 | 0.0005908793 |
| Phocea | 1.449534e-04 | 0.0004735835 |
| Ruminococcus_E | 1.382618e-04 | 0.0012752336 |
| UBA4855 | 1.362811e-04 | 0.0007776869 |
| CAG-145 | 1.215784e-04 | 0.0004454832 |
| Mailhella | 1.175204e-04 | 0.0005162449 |
| CAG-988 | 1.150383e-04 | 0.0008178711 |
| Marseille-P4683 | 1.140905e-04 | 0.0005092329 |
| AM07-15 | 1.059455e-04 | 0.0004745690 |
| Phascolarctobacterium | 1.005920e-04 | 0.0007816980 |
| Clostridium | 9.595775e-05 | 0.0005366982 |
| Anaerostipes | 8.894740e-05 | 0.0004351045 |
| Parasutterella | 8.207495e-05 | 0.0007872353 |
| CAG-41 | 7.878665e-05 | 0.0007556950 |
| Absicoccus | 6.676847e-05 | 0.0002502435 |
| Levilactobacillus | 5.757608e-05 | 0.0005522504 |
genus_arrange <- genus_summary %>%
group_by(genus) %>%
summarise(mean=sum(relabun)) %>%
filter(genus != "g__")%>%
arrange(-mean) %>%
select(genus) %>%
mutate(genus= sub("^g__", "", genus)) %>%
pull()
#Per day
genus_summary %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~Origin)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")